tbuckley/cabot-search huggingface dataset:
Predictive models in emergency medicine and their missing data strategies: a systematic review
Authors: Emilien Arnaud, Mahmoud Elbattah, Christine Ammirati, Gilles Dequen, Daniel Aiham Ghazali
Journal: npj Digital Medicine (2023)

Abstract In the field of emergency medicine (EM), the use of decision support tools based on artificial intelligence has increased markedly in recent years. In some cases, data are omitted deliberately and thus constitute “data not purposely collected” (DNPC). This accepted information bias can be managed in various ways: dropping patients with missing data, imputing with the mean, or using automatic techniques (e.g., machine learning) to handle or impute the data. Here, we systematically reviewed the methods used to handle missing data in EM research. A systematic review was performed after searching PubMed with the query “(emergency medicine OR emergency service) AND (artificial intelligence OR machine learning)”. Seventy-two studies were included in the review. The trained models variously predicted diagnosis in 25 (35%) publications, mortality in 21 (29%) publications, and probability of admission in 21 (29%) publications. Eight publications (11%) predicted two outcomes. Only 15 (21%) publications described their missing data. DNPC constitute the “missing data” in EM machine learning studies. Although DNPC have been described more rigorously since 2020, the descriptions in the literature are not exhaustive, systematic or homogeneous. Imputation appears to be the best strategy but requires more time and computational resources. To increase the quality and the comparability of studies, we recommend inclusion of the TRIPOD checklist in each new publication, summarizing the machine learning process in an explicit methodological diagram, and always publishing the area under the receiver operating characteristics curve—even when it is not the primary outcome.
Contrasting Patterns of Single Nucleotide Polymorphisms and Structural Variation Across Multiple Invasions
Authors: Katarina C Stuart, Richard J Edwards, William B Sherwin, Lee A Rollins
Journal: Molecular Biology and Evolution (2023)

Abstract Genetic divergence is the fundamental process that drives evolution and ultimately speciation. Structural variants (SVs) are large-scale genomic differences within a species or population and can cause functionally important phenotypic differences. Characterizing SVs across invasive species will fill knowledge gaps regarding how patterns of genetic diversity and genetic architecture shape rapid adaptation under new selection regimes. Here, we seek to understand patterns in genetic diversity within the globally invasive European starling, Sturnus vulgaris. Using whole genome sequencing of eight native United Kingdom (UK), eight invasive North America (NA), and 33 invasive Australian (AU) starlings, we examine patterns in genome-wide SNPs and SVs between populations and within Australia. Our findings detail the landscape of standing genetic variation across recently diverged continental populations of this invasive avian. We demonstrate that patterns of genetic diversity estimated from SVs do not necessarily reflect relative patterns from SNP data, either when considering patterns of diversity along the length of the organism's chromosomes (owing to enrichment of SVs in subtelomeric repeat regions), or interpopulation diversity patterns (possibly a result of altered selection regimes or introduction history). Finally, we find that levels of balancing selection within the native range differ across SNP and SV of different classes and outlier classifications. Overall, our results demonstrate that the processes that shape allelic diversity within populations is complex and support the need for further investigation of SVs across a range of taxa to better understand correlations between often well-studied SNP diversity and that of SVs.
Nanoparticle-mediated targeting of the fusion gene RUNX1/ETO in t(8;21)-positive acute myeloid leukaemia
Authors: Hasan Issa, Laura E. Swart, Milad Rasouli, Minoo Ashtiani, Sirintra Nakjang, Nidhi Jyotsana, Konstantin Schuschel, Michael Heuser, Helen Blair, Olaf Heidenreich
Journal: Leukemia (2023)

Abstract A hallmark of acute myeloid leukaemias (AMLs) are chromosomal rearrangements that give rise to novel leukaemia-specific fusion genes. Most of these fusion genes are both initiating and driving events in AML and therefore constitute ideal therapeutic targets but are challenging to target by conventional drug development. siRNAs are frequently used for the specific suppression of fusion gene expression but require special formulations for efficient in vivo delivery. Here we describe the use of siRNA-loaded lipid nanoparticles for the specific therapeutic targeting of the leukaemic fusion gene RUNX1/ETO . Transient knockdown of RUNX1/ETO reduces its binding to its target genes and alters the binding of RUNX1 and its co-factor CBFβ. Transcriptomic changes in vivo were associated with substantially increased median survival of a t(8;21)-AML mouse model. Importantly, transient knockdown in vivo causes long-lasting inhibition of leukaemic proliferation and clonogenicity, induction of myeloid differentiation and a markedly impaired re-engraftment potential in vivo. These data strongly suggest that temporary inhibition of RUNX1/ETO results in long-term restriction of leukaemic self-renewal. Our results provide proof for the feasibility of targeting RUNX1/ETO in a pre-clinical setting and support the further development of siRNA-LNPs for the treatment of fusion gene-driven malignancies.
Bear essentials
Authors: Tim Caro
Journal: Trends in Genetics (2023)

Strangely, American black bears come in many colours. New work by Puckett et al. shows that a missense alteration in the gene encoding tyrosinase-related protein 1 (TYRP1) likely interferes with melanin synthesis and is responsible for the cinnamon colour variant in the southwest USA. However, the adaptive significance of colour polymorphisms in this large carnivore remains opaque.
A micro-sized vaccine based on recombinant Lactiplantibacillus plantarum fights against SARS-CoV-2 infection via intranasal immunization
Authors: Letian Li, Jiayi Hao, Yuhang Jiang, Pengfei Hao, Yuwei Gao, Jing Chen, Guoqing Zhang, Ningyi Jin, Maopeng Wang, Chang Li
Journal: Acta Pharmaceutica Sinica B (2023)

COVID-19 has globally spread to burden the medical system. Even with a massive vaccination, a mucosal vaccine offering more comprehensive and convenient protection is imminent. Here, a micro-sized vaccine based on recombinant
Protopanaxadiol manipulates gut microbiota to promote bone marrow hematopoiesis and enhance immunity in cyclophosphamide‐induced immunosuppression mice
Authors: Yuru Cao, Ben Liu, Wenzhen Li, Feng Geng, Xue Gao, Lijun Yue, Huiping Liu, Congying Liu, Zhenguo Su, Junhong Lü, Xiaohong Pan
Journal: MedComm (2023)

Protopanaxadiol (PPD) has potential immunomodulatory effects, but the underlying mechanism remains unclear. Here, we explored the potential roles of gut microbiota in the immunity regulation mechanisms of PPD using a cyclophosphamide (CTX)-induced immunosuppression mouse model. Our results showed that a medium dose of PPD (PPD-M, 50 mg/kg) effectively ameliorated the immunosuppression induced by CTX treatment by promoting bone marrow hematopoiesis, increasing the number of splenic T lymphocytes and regulating the secretion of serum immunoglobulins and cytokines. Meanwhile, PPD-M protected against CTX-induced gut microbiota dysbiosis by increasing the relative abundance of
Validity evidence for observational ERCP competency assessment tools: a systematic review
Authors: Catharine M. Walsh, Samir C. Grover, Rishad Khan, Hoomam Homsi, Nikko Gimpaya, James Lisondra, Nasruddin Sabrie, Reza Gholami, Rishi Bansal, Michael A. Scaffidi, David Lightfoot, Paul D. James, Keith Siau, Nauzer Forbes, Sachin Wani, Rajesh N. Keswani
Journal: Endoscopy (2023)

Background Assessment of competence in endoscopic retrograde cholangiopancreatography (ERCP) is critical for supporting learning and documenting attainment of skill. Validity evidence supporting ERCP observational assessment tools has not been systematically evaluated. Methods We conducted a systematic search using electronic databases and hand-searching from inception until August 2021 for studies evaluating observational assessment tools of ERCP performance. We used a unified validity framework to characterize validity evidence from five sources: content, response process, internal structure, relations to other variables, and consequences. Each domain was assigned a score of 0–3 (maximum score 15). We assessed educational utility and methodological quality using the Accreditation Council for Graduate Medical Education framework and the Medical Education Research Quality Instrument, respectively. Results From 2769 records, we included 17 studies evaluating 7 assessment tools. Five tools were studied for clinical ERCP, one for simulated ERCP, and one for simulated and clinical ERCP. Validity evidence scores ranged from 2 to 12. The Bethesda ERCP Skills Assessment Tool (BESAT), ERCP Direct Observation of Procedural Skills Tool (ERCP DOPS), and The Endoscopic Ultrasound (EUS) and ERCP Skills Assessment Tool (TEESAT) had the strongest validity evidence, with scores of 10, 12, and 11, respectively. Regarding educational utility, most tools were easy to use and interpret, and required minimal additional resources. Overall methodological quality (maximum score 13.5) was strong, with scores ranging from 10 to 12.5. Conclusions The BESAT, ERCP DOPS, and TEESAT had strong validity evidence compared with other assessments. Integrating tools into training may help drive learners’ development and support competency decision making.
Optimal Intensity and Duration of Walking Rehabilitation in Patients With Chronic Stroke
Authors: Pierce Boyne, Sandra A. Billinger, Darcy S. Reisman, Oluwole O. Awosika, Sofia Buckley, Jamiah Burson, Daniel Carl, Matthew DeLange, Sarah Doren, Melinda Earnest, Myron Gerson, Madison Henry, Alli Horning, Jane C. Khoury, Brett M. Kissela, Abigail Laughlin, Kiersten McCartney, Thomas McQuaid, Allison Miller, Alexandra Moores, Jacqueline A. Palmer, Heidi Sucharew, Elizabeth D. Thompson, Erin Wagner, Jaimie Ward, Emily Patton Wasik, Alicen A. Whitaker, Henry Wright, Kari Dunning
Journal: JAMA Neurology (2023)

For walking rehabilitation after stroke, training intensity and duration are critical dosing parameters that lack optimization.
Stepping Closer to Precision Rehabilitation
Authors: David J. Lin, Joel Stein
Journal: JAMA Neurology (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Neurology HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Neurology journal
Computed Tomography-Defined Sarcopenia in Outcomes of Patients with Unresectable Hepatocellular Carcinoma Undergoing Radioembolization: Assessment with Total Abdominal, Psoas, and Paraspinal Muscles
Authors: Chih-Horng Wu, Ming-Chih Ho, Chien-Hung Chen, Ja-Der Liang, Kai-Wen Huang, Mei-Fang Cheng, Chih-Kai Chang, Chia-Hung Chang, Po-Chin Liang
Journal: Liver Cancer (2023)

Introduction: Sarcopenia is an adverse prognostic factor in patients with liver cirrhosis and hepatocellular carcinoma (HCC). Image-based sarcopenia assessment allows a standardized method to assess abdominal skeletal muscle. However, which is an index muscle for sarcopenia remains unclear. Therefore, we investigated whether sarcopenia defined according to different muscle groups with computed tomography (CT) scans can predict the prognosis of HCC after radioembolization. Methods: In this retrospective study, we analyzed patients who underwent radioembolization for unresectable HCC between January 2010 and December 2019. Before treatment, the total abdominal muscle (TAM), psoas muscle (PM), and paraspinal muscle (PS) areas were evaluated using a single CT slice at the third lumbar vertebra. In previous studies, sarcopenia was determined using the TAM, PM, and PS after stratifying by sex. Finally, we investigated each muscle-defined sarcopenia to decide whether or not it can serve as a prognostic factor for overall survival (OS). Results: We included 92 patients (74 men and 18 women). TAM, PM, and PS areas were significantly higher in the men than in the women (all p &amp;lt; 0.05). The patients with sarcopenia defined using PM, but not TAM and PS, exhibited significantly poorer OS than those without sarcopenia (median 15.3 vs. 23.8 months, p = 0.034, 0.821, and 0.341, respectively). After adjustment for clinical variables, such as body mass index, liver function, alpha-fetoprotein level, clinical staging, treatment response, and posttreatment curative therapy, PM-defined sarcopenia (hazard ratio: 1.899, 95% confidence interval: 1.087–3.315) remained an independent predictor for the poor OS. Conclusion: CT-assessed sarcopenia defined using PM was an independent prognostic factor for the poorer prognosis of unresectable HCC after radioembolization.
Hyperfractionation compared with standard fractionation in intensity-modulated radiotherapy for patients with locally advanced recurrent nasopharyngeal carcinoma: a multicentre, randomised, open-label, phase 3 trial
Authors: Rui You, You-Ping Liu, Yu-Long Xie, Chao Lin, Chong-Yang Duan, Dong-Ping Chen, Yi Pan, Bin Qi, Xiong Zou, Ling Guo, Jing-Yu Cao, Yi-Nuan Zhang, Zhi-Qiang Wang, Yong-Long Liu, Yan-Feng Ouyang, Kai Wen, Qi Yang, Ruo-Qi Xie, Hui-Feng Li, Xiao-Tong Duan, Xi Ding, Lan Peng, Si-Yuan Chen, Jiong-Lin Liang, Zheng-Kai Feng, Tian-Liang Xia, Rui-Ling Xie, Rou Jiang, Chen-Mei Gu, Rong-Zeng Liu, Rui Sun, Xin Yang, Li-Zhi Liu, Li Ling, Qing Liu, Wai Tong Ng, Yi-Jun Hua, Pei-Yu Huang, Ming-Yuan Chen
Journal: The Lancet (2023)
An Integrated Digital Health Care Platform for Diabetes Management With AI-Based Dietary Management: 48-Week Results From a Randomized Controlled Trial
Authors: You-Bin Lee, Gyuri Kim, Ji Eun Jun, Hyunjin Park, Woo Je Lee, You-Cheol Hwang, Jae Hyeon Kim
Journal: Diabetes Care (2023)

OBJECTIVE We investigated the efficacy of an integrated digital health care platform with artificial intelligence (AI)–based dietary management in adults with type 2 diabetes (T2D). RESEARCH DESIGN AND METHODS In this 48-week, open-label, randomized, multicenter clinical trial, overweight or obese adults with T2D were randomly assigned to one of three groups in a 1:1:1 ratio: group A received routine diabetes care; group B used the digital integrated health care platform by themselves; and group C used the platform with feedback from medical staff and intermittently applied personal continuous glucose monitoring. The primary end point was the difference of change in HbA1c from baseline to 24 weeks between groups A and B, while secondary end points included changes in HbA1c from baseline to 48 weeks and changes in body weight during follow-up. RESULTS A total of 294 participants were randomly assigned to group A (n = 99), B (n = 97), or C (n = 98). The decreases in HbA1c from baseline to 24 and 48 weeks in group B (−0.32 ± 0.58% to 24 weeks and −0.28 ± 0.56% to 48 weeks) and group C (−0.49 ± 0.57% to 24 weeks and −0.44 ± 0.62% to 48 weeks) were significantly larger than those in group A (−0.06 ± 0.61% to 24 weeks and 0.07 ± 0.78% to 48 weeks). Groups B and C exhibited greater weight loss than group A from baseline to 24 weeks, and group C demonstrated more weight loss than group A from baseline to week 48. CONCLUSIONS Among adults with T2D, use of an integrated digital health care platform with AI-driven dietary management resulted in better glycemia and more weight loss.
Safety and efficacy of vanzacaftor–tezacaftor–deutivacaftor in adults with cystic fibrosis: randomised, double-blind, controlled, phase 2 trials
Authors: Ahmet Z Uluer, Gordon MacGregor, Pilar Azevedo, Veronica Indihar, Claire Keating, Marcus A Mall, Edward F McKone, Bonnie W Ramsey, Steven M Rowe, Ronald C Rubenstein, Jennifer L Taylor-Cousar, Elizabeth Tullis, Lael M Yonker, Chenghao Chu, Anna P Lam, Nitin Nair, Patrick R Sosnay, Simon Tian, Fredrick Van Goor, Lakshmi Viswanathan, David Waltz, Linda T Wang, Yingmei Xi, Joanne Billings, Alexander Horsley, Alexander Horsley, Edward F. Nash, Marleen Bakker, Renske van der Meer, Petrus Merkus, Christof Majoor, Karen McCoy, Joanne Billings, Krishna Pancham, James Tolle, Bryon Quick, Ahmet Uluer, Emily DiMango, Adupa Rao, Santiago Reyes, Ross Klingsberg, Celeste Barreto, Victor Ortega, Donna Willey-Courand, Carsten Schwarz, Sivagurunathan Sutharsan, Rainald Fischer, Jane Davies, Jamie Duckers, Alexander Horsley, Simon Doe, Edward F. Nash, Marleen Bakker, Harry Heijerman, Renske van der Meer, Petrus Merkus, Christof Majoor, George M. Solomon, Christian Merlo, Jennifer Griffonnet, Joseph Pilewski, Jordan Dunitz, Saba Sheikh, Ronald C. Rubenstein, Daniel B. Rosenbluth, Theodore Liou, Maria Indihar, Krishna Pancham, Lael Yonker, Samya Nasr, Jennifer Griffonnet, Cynthia D. Brown, Gregory S. Sawicki, Jennifer Ruddy, Emily DiMango, Bryan Garcia, Andrew Braun, Alex H. Gifford, Nighat Mehdi, Maria Tupayachi Ortiz, Raksha Jain, Francisco J. Calimano, Jimmy Johannes, Cori L. Daines, Jason Fullmer, Joel Mermis, Christopher Barrios, Ngoc Ly, Brian P. Casserly, Stephan Eisenmann, Helge Hebestreit, Alexander Kiefer, Sivagurunathan Sutharsan, Rainald Fischer, Gordon MacGregor, Daniel Peckham, Martin Ledson, Eva Van Braeckel, Petrus Merkus, Noel Gerard McElvaney, Edward McKone, Barry Plant, Lucy Burr, Daniel J. Smith, Peter Middleton, John Wilson
Journal: The Lancet Respiratory Medicine (2023)
Cancer Screening in the United States During the Second Year of the COVID-19 Pandemic
Authors: Jessica Star, Priti Bandi, Rebecca L. Siegel, Xuesong Han, Adair Minihan, Robert A. Smith, Ahmedin Jemal
Journal: Journal of Clinical Oncology (2023)

To examine whether cancer screening prevalence in the United States during 2021 has returned to prepandemic levels using nationally representative data.
Functional Engagement of the PD-1/PD-L1 Complex But Not PD-L1 Expression Is Highly Predictive of Patient Response to Immunotherapy in Non–Small-Cell Lung Cancer
Authors: Lissete Sánchez-Magraner, Juan Gumuzio, James Miles, Nicole Quimi, Purificación Martínez del Prado, María Teresa Abad-Villar, Fernando Pikabea, Laura Ortega, Carmen Etxezarraga, Salvador Martín-Algarra, María D. Lozano, Mónica Saiz-Camin, Mikel Egurrola-Izquierdo, Inmaculada Barredo-Santamaría, Alberto Saiz-López, Jenifer Gomez-Mediavilla, Nerea Segues-Merino, María Aranzazu Juaristi-Abaunz, Ander Urruticoechea, Erica J. Geraedts, Kim van Elst, Niels J.M. Claessens, Antoine Italiano, Christopher J. Applebee, Sandra del Castillo, Charles Evans, Fernando Aguirre, Peter J. Parker, Véronique Calleja
Journal: Journal of Clinical Oncology (2023)

In many cancers, the expression of immunomodulatory ligands leads to immunoevasion, as exemplified by the interaction of PD-L1 with PD-1 on tumor-infiltrating lymphocytes. Profound advances in cancer treatments have come with the advent of immunotherapies directed at blocking these immuno-suppressive ligand-receptor interactions. However, although there has been success in the use of these immune checkpoint interventions, correct patient stratification for these therapies has been challenging.To address this issue of patient stratification, we have quantified the intercellular PD-1/PD-L1 interaction in formalin-fixed paraffin-embedded tumor samples from patients with non-small cell lung carcinoma, using a high-throughput automated quantitative imaging platform (quantitative functional proteomics [QF-Pro]).The multisite blinded analysis across a cohort of 188 immune checkpoint inhibitor-treated patients demonstrated the intra- and intertumoral heterogeneity of PD-1/PD-L1 immune checkpoint engagement and notably showed no correlation between the extent of PD-1/PD-L1 interaction and PD-L1 expression. Importantly, PD-L1 expression scores used clinically to stratify patients correlated poorly with overall survival; by contrast, patients showing a high PD-1/PD-L1 interaction had significantly better responses to anti-PD-1/PD-L1 treatments, as evidenced by increased overall survival. This relationship was particularly strong in the setting of first-line treatments.The functional readout of PD-1/PD-L1 interaction as a predictive biomarker for the stratification of patients with non-small-cell lung carcinoma, combined with PD-L1 expression, should significantly improve the response rates to immunotherapy. This would both capture patients excluded from checkpoint immunotherapy (high PD-1/PD-L1 interaction but low PD-L1 expression, 24% of patients) and additionally avoid treating patients who despite their high PD-L1 expression do not respond and suffer from side effects.
<i>DPYD</i> Testing: Time to Put Patient Safety First
Authors: Sharyn D. Baker, Susan E. Bates, Gabriel A. Brooks, William L. Dahut, Robert B. Diasio, Wafik S. El-Deiry, William E. Evans, William D. Figg, Dan L. Hertz, J. Kevin Hicks, Suneel Kamath, Pashtoon Murtaza Kasi, Todd C. Knepper, Howard L. McLeod, Peter H. O'Donnell, Mary V. Relling, Michelle A. Rudek, Tristan M. Sissung, D. Max Smith, Alex Sparreboom, Sandra M. Swain, Christine M. Walko
Journal: Journal of Clinical Oncology (2023)

In 2018, a patient received capecitabine without prior testing for dihydropyrimidine dehydrogenase (DPYD) and later presented with vomiting, rash, and diarrhea.The hospital failed to provide uridine triacetate in a timely fashion, and the patient died.The patient's widow filed a wrongful death lawsuit against Oregon Health Sciences University (OHSU) and assisted in the formation of a nonprofit organization to advocate for DPYD testing for fluoropyrimidines.A settlement for $1 million US dollars was reached requiring OHSU oncologists to undergo education about DPYD testing and inform their patients about its availability. 1Clinical practice guidelines from the National Comprehensive Cancer Network (NCCN) and ASCO still do not support testing for DPYD genetic variants before fluoropyrimidine chemotherapy.The US Food and Drug Administration (FDA) package inserts for capecitabine and fluorouracil (FU) acknowledge patients with dihydropyrimidine dehydrogenase protein (DPD) deficiency have increased risk of life-threatening toxicity; however, instead of recommending preemptive testing, they posit an unlikely scenario in which patients who have known DPD deficiency should discuss it with their physicians. 2,3The European Medicines Agency, the French National Agency for the Safety of Medicines and Health Products, and the Medicines and Healthcare products Regulatory Agency have each approved guidelines for preemptive DPYD testing for patients treated with fluoropyrimidines.